Intercalation, with DNA

Quinacrine concentrates in the scolex of the parasite and causes the muscles needed for holding onto the intestinal wall to relax. The worms are stained yellow and pass from the body, still aUve. Quinacrine can intercalate with DNA and inhibit nucleic acid synthesis. It creates fluorescent bands in deoxyadenylate—deoxythmidylate-rich regions of DNA and has been used as a stain in the study of human genetics. 

Oxygen-free reactions of psoralens, when in close proximity to the target, proceed via the first excited states in which the 3,4-and the 4, 5 7r-bonds of the pyrone and furan moieties, respectively, can undergo C4-cyclization reactions with, e.g., unsaturated bonds of lipids, or the C5=C6 double bonds of thymine in DNA. In reactions with DNA the psoralen is believed to intercalate with DNA in the dark. Subsequent irradiation at 400 nm usually leads to furan-side 4, 5 -monoadduct formation, whereas irradiation at 350 nm increases the formation of crosslinks in which the furan and pyrone rings form C4 cycloadducts to thymines on opposite strands [95], Subsequent irradiation of the 4, 5 -monoadducts at 350 nm leads to formation of crosslinks and conversion into pyrone-side 3,4-monoadducts. Shorter wave-... 

QSAR (4) would appear to be a useful measure of whether other similar polycyclic aromatics can intercalate with DNA. Two pyrene-containing mutagens A-butoxy-A-(l-pyrenecarboxoyloxy)acetamide and A-butoxy-A-(l-pyreneacetoxy)acetamide... 

In 1984, Giibble et al. reported for the first time a novel l,10-bis-(6-methyl-5H-benzo[fc]carbazol-ll-yl)decane (469) which has potential bifunctional nucleic acid intercalating properties (406). To function as anti-tumor active drugs, one of the most important cytostatic mechanisms of action of coplanar annelated polycyclic compounds is their intercalation with DNA (405). Ten years later, Kucklander et al. studied a series of 5H-benzo[ 7]carbazole quinone derivatives for their cytotoxic activity against colon and lung cancer cells, and found that the heteroannelated 5H-benzo[ 7]carbazole quinone derivative 470 was the most active among the various analogs (407) (Scheme 4.2). 

Bleomycin intercalates between bases (f d ouble-stranded DNS(34). In this connection, it is interesting that phleomycin which has the dihydrobithiazole moiety, does not intercalate with DNA (33). It causes more single-strand scission than double-strand scission (30). 

In Fig. 1 various targets of some important cytostatic agents are depicted. Their main mechanisms of action can be briefly summarized as follows. Pentostatin blocks purine nucleotides by inhibiting adenosine deaminase. 6-Mercaptopurine and 6-thioguanine inhibit purine ring biosynthesis and they inhibit nucleotide interconversions. Methotrexate by inhibiting dihydrofolate reduction blocks thymidine monophosphate and purine synthesis. 5-Fluorouracil also blocks thymidine monophosphate synthesis. Dactinomycin, daunorubicin, doxorubicin and mitoxantrone intercalate with DNA and inhibit RNA synthesis. L-asparaginase deaminates... 

Chloroquine (Aralen) is one of several 4-aminoquino-line derivatives that display antimalarial activity. Chloroquine is particularly effective against intraerythrocytic forms because it is concentrated within the parasitized erythrocyte. This preferential drug accumulation appears to occur as a result of specific uptake mechanisms in the parasite. Chloroquine appears to work by intercalation with DNA, inhibition of heme polymerase or by interaction with Ca++-calmodulin-mediated mechanisms. It also accumulates in the parasite s food vacuoles, where it inhibits peptide formation and phospholipases, leading to parasite death. 

Mitoxantrone (Novantrone) is a synthetic anthraquinone that is structurally and mechanistically related to the an-thracyclines. It intercalates with DNA and produces single-strand DNA breakage. It is cross-resistant with dox-... 

Drug-receptor interactions often involve CT complex formation. Examples include the reactions of antimalarials with their receptors and of some antibiotics that intercalate with DNA. The CT energy is proportional to the ionization potential of the donor and the electron affinity of the receptor, but is usually no higher than about 30 kJ/mol. 

Psoralens must be photoactivated by long-wavelength ultraviolet light in the range of 320-400 nm (ultraviolet A [UVA]) to produce a beneficial effect. Psoralens intercalate with DNA and, with subsequent UVA irradiation, cyclobutane adducts are formed with pyrimidine bases. Both monofunctional and bifunctional adducts may be formed, the latter causing interstrand cross-links. These DNA photoproducts may inhibit DNA synthesis. The major long-term risks of psoralen photochemotherapy are cataracts and skin cancer. 

More recent studies have indicated a probable mechanism that relies on the interaction of thalidomide with DNA. The phthalimide double-ring structure (Fig. 7.74) is relatively flat and can intercalate with DNA forming a stacked complex. Furthermore, observations were made that thalidomide... 

Doxorubicin intercalates with DNA, causing an inhibition of RNA synthesis.2... 

A variety of alkaloids bind to or intercalate with DNA or DNA/RNA processing enzymes and affect either transcription or replication (quinine, harmane alkaloids, melinone, berberine), act at the level of DNA and RNA polymerases (vinblastine, coralyne, avicine), inhibit protein synthesis (sparteine, tubulosine, vincrastine, lupanine), attack electron chains (pseudane, capsaicin, solenopsine), disrupt biomembranes and transport processes (berbamine, ellipticine, tetrandrine), and inhibit ion channels and pumps (nitidine, caffeine, saxitoxin). In addition, these natural products attack a variety of other systems that can result in serious biochemical destabilization... 

Melting point determination. If compounds intercalate with DNA, then the melting point is shifted to higher temperatures.21,25 70 pM Sinapis DNA was incubated in TE-buffer (pH 7.4) with 70 pM alkaloids for 30 min at 22°C. Then the temperature was increased by 1°C/min to 90 °C and the absorption was continuously... 

II. Methylgreen assay. Methylgreen (MG) binds to DNA and bound MG displays an absorption maximum at 642 nm, whereas free MG shows no absorption at this wavelength.4,18 When alkaloids bind or intercalate with DNA, then MG is released, which can be measured as a decrease of optical density at 642 nm. 70 pM DNA-methylgreen (Sigma, USA) was incubated in the dark in 20 mM Tris-HCI (pH 7.4) together with up to 5 mM alkaloids. After 24 h the OD642 of untreated controls and treated samples was determined.19... 

A variety of plant substances with planar, polycyclic, aromatic structures can intercalate with DNA, examples being the quinoline alkaloid camptothecin and the furanocoumarin phenolic psoralen (Table 12.1). A variety of plant-derived anthraquinones and naphthoquinones bind to DNA and it is notable that the structurally related anthraquinones mitox-antrone and adriamycin are clinically employed as anticancer drugs (Table 12.1). DNA-binding compounds that interfere with DNA repair, DNA replication and gene expression are cytotoxic and have potential as anticancer agents (see Chapter 9). 

Ethidium bromide is a popular stain for nucleic acids, and dye intercalated with DNA during electrophoresis fluoresces when illuminated with UV light. 

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